Sacramento County Public Health Laboratory Test Menu and Specimen Collection Manual 2021

Sacramento County Public Health Laboratory
     Test Menu and Specimen Collection Manual
                      2021

In addition to the available tests listed in this manual Sacramento County Public
Health Laboratory (SCPHL) provides access to reference services at the
California Department of Public Health State Laboratory and the Centers for
Disease Control and Prevention (CDC).
Contact SCPHL at (916) 874-9231 with any questions regarding tests listed
in this guide or tests available at MDL, VRDL or the CDC.

Acid Fast Culture and Smear (Mycobacteriology)

CPT Code: 87015 (Method, Specimen Concentration), 87206 (Method,
Fluorescent stain), 87116 (Method, Culture)

Specimen Collection: (Collect specimens before antimicrobial therapy)

1. Sputum
      a. Rinse the mouth with water before sputum is collected to minimize
         residual food particles, mouthwash, and oral drugs that might
         contaminate the specimen or inhibit growth of any acid-fast bacilli
         present.
      b. Saliva and nasopharyngeal discharge are not sputum.
      c. Collect only the exudative material brought up from the lungs after a
         deep, productive cough.
      d. Early morning specimens, preferably 5 - 10 ml each, should be
        collected on three consecutive days. A volume of at least 3 ml is desired
        for testing.

2. Blood
      a. A sample of 5 - 8 ml may be collected in either of the following
         sterile anticoagulant Vacutainer® tubes:
         Yellow top containing sodium polyanethol sulfonate (SPS)
         Green top containing sodium heparin
      b. Blood collected in EDTA tubes or coagulated blood are NOT
         acceptable.
      c. Blood specimens are stored at room temperature if they cannot be
         immediately transported or processed for testing.

3. Body Fluids
      a. Collect all fluids in sterile containers with screw-cap lids.
      b. Abdominal fluid (peritoneal, paracentesis, dialysis, bile) 10 - 15 ml
      c. Chest fluids (pleural, thoracentesis, empyema) 10 - 15 ml
      d. Exudates (transudates, drainages, ulcers) 3 - 5 ml
      e. Other fluids (pericardial, synovial, joint) 2 - 3 ml

4. Bone
      a. For large, clean bone fragments with no tissue attached, add sterile
          saline to completely cover the specimen and vortex vigorously for 1 - 2
          minutes.
      b. For large bone fragments with tissue attached, scrape as much
          tissue as possible from the bone and process the tissue. Cover
         remaining bone with saline, vortex and inoculate saline to media.
      c. Transport and store at room temperature

5. CSF
      a. As much fluid as possible is aseptically collected by aspiration or
        during surgical procedures, as only small numbers of organisms may be
        present. The recommended volume is 2 ml.
      b. Transport and store at room temperature.

6. Gastric Lavage Fluid
       a. Aspiration of swallowed sputum from the stomach may be
          necessary for patients with minimal disease, infants, young children,
          and adults who are unable to cooperate with sputum induction
          procedures.
       b. Fasting, early morning specimens are optimal.
       c. A volume of 20 - 30 ml is recommended.
       d. If the specimen cannot be processed within 4 hours, the collection
          bottle should contain about 100 mg of sodium carbonate or another
          alkaline buffer salt. This reduces long-term exposure of any
          mycobacteria to the stomach acid, which is detrimental to organism
          recovery and detection.

7. Stool
    a. Mix 2 grams (marble-size) of stool with 10 ml of saline.
    b. Filter with 4 - 6 layers of gauze into a 50 ml centrifuge tube, and submit
       the tube.

8. Swabs
    a. Draining sinus site
    b. Swabs are not optimal for the recovery of mycobacteria because of limited
       surface area and hydrophobic nature of mycobacteria

9. Tissue
    a. At least 1 g or 1 mm3 of tissue should be collected into a sterile
       container without fixatives or preservatives.
    b. To protect the tissue from drying, a small amount of sterile saline may
       be added.

10. Urine
       A series of three, early morning, cleanly voided, midstream
       specimens collected on consecutive days is superior to a 24 hour pooled
       specimen. A volume of 15 ml is recommended.

11. Wounds
      Skin lesions, granulomas, ulcers, subcutaneous nodules, or
      anything related to an extremity may be sampled if the physician suspects
      M. marinum and/or M. ulcerans. Aseptically collect as much material as
      possible.

Transportation and Storage:
Transport specimens to the laboratory at 4oC, within 24 hours.
Refrigerate specimens at 4oC if delivery is delayed.

Autoclave Sterilization Verification

CPT Code: None (Method, Culture)

Specimen Collection:
Send autoclave treated Sporampules along with an untreated ampule
from the same lot. Please record the lot number and expiration date of the
ampules on the specimen requisition form.

Transportation and Storage:
Transport as soon as possible at room temperature.

Chlamydia / Gonorrhea Nucleic Acid Amplified Test (NAAT)

CPT Code: 87491and 87591 (Method, NAAT)

Specimen Collection:
   1. Endocervical swab specimens
      a. Remove excess mucus from the cervical os and surrounding mucosa
          using the cleaning swab (white shaft swab in the package with red
          printing). Discard this swab after use.
      b. Insert the specimen collection swab (blue shaft swab in the package
          with green printing) into the endocervical canal.
      c. Gently rotate the swab clockwise for 10 - 30 seconds in the
          endocervical canal to ensure adequate sampling.
      d. Withdraw the swab carefully; avoid any contact with the vaginal
         mucosa.
      e. Remove the cap from the swab specimen transport tube and
         immediately place the specimen collection swab into the transport
         tube.
      f. Carefully break the swab shaft at the score line; use care to avoid
         splashing of the contents.
      g. Recap the swab specimen transport tube tightly.

  2. Male urethral swab specimens
      a. The patient should not have urinated for at least one hour prior to
          specimen collection.
      b. Insert the specimen collection swab (blue shaft swab in the package
         with the green printing) 2 - 4 cm into the urethra.
      c. Gently rotate the swab clockwise for 2 - 3 seconds in the urethra to
          ensure adequate sampling.
      d. Withdraw the swab carefully.
      e. Remove the cap from the swab specimen transport tube and
          immediately place the specimen collection swab into the specimen
          transport tube.
      f. Carefully break the swab shaft at the score line; use care to avoid
         splashing of the contents. Recap the specimen transport tube tightly.

3. Urine specimens (male or female)
    a. The patient should not have urinated for at least one hour prior to
       specimen collection.
    b. Direct patient to provide first-catch urine (approximately 20 - 30 ml of
       the initial urine stream) into a urine collection cup free of any
       preservatives. Collection of larger volumes of urine may result in
       specimen dilution that may reduce test sensitivity. Female patients
       should not cleanse the labial area prior to providing the specimen.
    c. Remove the cap and transfer 2 ml of urine into the urine specimen
       transport tube using the disposable pipette provided. The correct
       volume of urine has been added when the fluid level is between the
       black fill lines on the urine transport tube label.
    d. Re-cap the urine specimen transport tube tightly. This is now known
      as the processed urine specimen.

4. Throat and rectal specimens
    a. Partially open the multitest swab. Do not touch the soft tip or lay the
       swab down. Hold the swab with the thumb and forefinger in the middle
       of the shaft covering the black score line
    b. Insert the swab into the rectum 1 to 2 inches past the anal margin and
       rotate the swab 5 to 10 seconds
   c. Immediately place the swab into the transport tube and break the shaft
       at the score line. Tightly recap the tube and add patient information on
       the tubes label
   d. For throat specimens insert the swab ensuring contact with bilateral
       tonsils and posterior pharyngeal wall. Remove the swab without
       touching the cheek or tongue.
   e. Preparation of the swab, transport and labelling are the same as rectal
       specimen

   f. Urine Specimens: After collection, transport the processed urine
      specimens in the GENPROBE APTIMA urine specimen transport tube
      at 2° - 30°C and store at 2° - 30°C until tested. Processed urine
      specimens should be assayed within 30 days of collection. If longer
      storage is needed, freeze at -20° to -70°C for up to 90 days after
      collection. Urine samples that are still in the primary collection
      container must be transported to the lab at 2° - 30°C. Transfer the
      urine sample into the APTIMA urine specimen transport tube within 24

hours of collection. Store at 2° - 30°C and test within 30 days of
          collection.

4. Transportation and Storage:
      a. Swab specimens: After collection, transport and store the swab in the
         swab specimen transport tube at 2o to 30o C until tested. Specimens
         must be assayed with the APTIMA Combo 2 Assay within 60 days of
         collection. If longer storage is needed, freeze at -20oC to -70°C for up to
        90 days after collection.
       b.Urine Specimens: After collection, transport the processed urine
         specimens in the GENPROBE APTIMA urine specimen transport tube
         at 2°C to 30oC and store at 2°C to 30oC until tested. Processed urine
         specimens should be assayed within 30 days of collection. If longer
         storage is needed, freeze at -20oC to -70oC for up to 90 days after
         collection. Urine samples that are still in the primary collection
         container must be transported to the lab at 2°C to 30°C. Transfer the
         urine sample into the APTIMA urine specimen transport tube within 24
         hours of collection. Store at 2°C to 30oC and test within 30 days of
         collection.

Clearance: Specify enteric pathogen

CPT Code: 87045 (Method, Culture)

Specimen Collection:
  a. Collect stool and place in the Enteric Collection kit (supplied by the
      lab), or use a clean, sterile, plastic container. Transfer enough stool into
      the transport fluid so that the liquid level is raised to the red fill line.
      Thoroughly mix contents of the vial.
  b. Fill out a Title 17 submission form for this specimen type.

Transportation and Storage:
Transport to the laboratory at room temperature within 72 hours.

Culture for Identification (Bacterial, Fungal, Mycobacterial)
CPT Code: 87077 (Method, Culture)
Specimen Collection:
Complete a Title 17 submission form for this specimen type.
Cultures for identification should be submitted on screw-cap agar
slants appropriate to the organism. Cultures should be fully grown when
submitted, or delays in identification may result.
DO NOT SUBMIT CULTURES FOR IDENTIFICATION ON PLATE MEDIA
UNLESS ABSOLUTELY NECESSARY!
IF SUBMITTED, PLATES MUST BE SEALED COMPLETELY WITH TAPE
OR THEY MAY BE REJECTED.
Transportation and Storage:
Transport immediately to the laboratory at room temperature.

Dark-field Fresh Exudate – Syphilis Detection
CPT Code: 87166 (Method, Microscopic examination)
Specimen Collection:
Collect serous exudate from base of the lesion. Place specimen on
a microscope slide with cover slip.
(Special collection note: Contact the Laboratory BEFORE COLLECTION to make
arrangements for test interpretation by a microbiologist.)

Transportation and Storage:
Specimen MUST BE READ within 10 minutes of collection.

Drug Susceptibility (Antimicrobial Susceptibility Testing) (AST)

CPT Code: 87188 x 7 (M. tuberculosis isolates)

Specimen Collection:
Cultures for drug susceptibility should be submitted on screw-cap
agar slants appropriate to the organism. Cultures should be fully grown
when submitted, or delays in testing may result. DO NOT SUBMIT
CULTURES ON PLATE MEDIA.
Complete a Title 17 submission form for this specimen type.

Transportation and Storage:
Transport immediately to the laboratory at room temperature.

Enteric Screen: Salmonella/Shigella/E. coli O157/Shiga Toxin

CPT Code: 87045and 87046 (Method, Culture)

Specimen Collection:
Collect stool and place in the Enteric Collection kit (supplied by the
laboratory), or use a clean, sterile, plastic container. Transfer enough stool into
the transport fluid so that the liquid level is raised to the red fill line. Thoroughly
mix contents of the vial. If Vibrio is suspected notify the laboratory prior to
submission of specimen
Transportation and Storage:
1. Store and transport stool specimens in C&S medium at room
temperature within 24 hours. Specimens between 24 - 96 hours old may
be tested and the results qualified to reflect that excess transit time may
affect recovery of enteric pathogens.
2. Specimens in C&S medium, greater than 96 hours old, are
unsatisfactory for testing.
3. Unpreserved, fresh specimens must be received within 4 hours of
collection. Unpreserved specimens received 4 - 24 hours after collection
may be tested and the results qualified. Unpreserved specimens
received more than 24 hours after collection are unsatisfactory for
testing.
4. Multiple stool specimens collected on the same day are acceptable for
enteric culture.
5. Buffered glycerol saline is an unsatisfactory transport medium for the
isolation of Vibrio sp.
6. Urine specimens for isolation of Salmonella typhi must be received in a
sterile screw-top container within 24 hours of collection.
7. Rectal swabs are generally not satisfactory specimens except for
outbreaks of Shigella sp. However, if a patient is unable to submit a
stool specimen, a rectal swab may be tested and the results qualified as
“scant specimen.” Rectal swabs are collected in Amies charcoal

transport media, stored at room temperature, and may be tested up to 72 hours
after collection.

Fungal/yeast Culture and ID
CPT Code: 87101 (Method, Culture)
Specimen Collection:
Skin, hair and nail specimens should be collected into a sterile
container. Thoroughly disinfect the area around skin and nails with 70%
alcohol before collection.
Please contact the laboratory for specific instructions, as collection
and transport procedures vary widely for various specimen types and
suspected etiologic agents.
Transportation and Storage:
Transport skin, hair, and nail specimens in a fungus collection kit;
specimens are stable at room temperature.

Gonorrhea Culture Screen
CPT Code: 87081 (Method, Culture), 87077 (Pathogen rule-out)
Specimen Collection:
Specimens are collected using a sterile Dacron, rayon or calcium
alginate swab. Cotton swabs may contain substances that are toxic to the
organism and are not recommended. Acceptable specimens for culture
include genital, oral and rectal sites.
Transportation and Storage:
Specimens are inoculated onto a GC pill plate, and immediately
placed into a zipper lock bag with a CO2 generating tablet. The plate should
be incubated within 30 minutes at 35º - 37ºC, and transported to the
laboratory within 72 hours of collection.
Place specimens collected by swab into Amies transport media,
and transport at room temperature to the laboratory within 8 hours. GC is
viable in Amies transport media for only 8 hours.

HIV Antibody Screening (Serum / Plasma)
CPT Code: 86701 (Method, Enzyme immunoassay)

Specimen Collection:
Serum, plasma, or cadaveric serum specimens may be used in the
test. The following anticoagulants have all been evaluated and found to be
acceptable: EDTA, sodium and lithium heparin, sodium citrate, CPD, CPDA-
1, and ACD.
Cadaveric serum samples may be tested; please contact the
laboratory for more information.
Transportation and Storage:
Transport serum and plasma specimens at 2° - 8°C within 7 days. If
transport is delayed, specimens should be frozen at -20°C or colder.
Specimens should not be used if they have incurred more than 5 freeze-thaw
cycles.

Influenza Virus PCR w/ subtyping
CPT Code: 87502 x 2 (Method, real-time PCR), 87503 x 4
Specimen collection:
Specimens should be collected as soon as possible after onset of
symptoms and before anti-viral treatment. Please keep in mind the
following guidelines:
 a. Nasal aspirates or nasal washes are the preferred specimens. Collect in
    a sterile, screw-capped container. Bronchoalveolar lavage and tracheal
    aspirates are also acceptable.
b. Close off both ports of Lukens traps and aspiration tubes by securely
connecting the vacuum tube to both ports.
Small tipped Dacron or polyester nasopharyngeal swabs can be used for
specimen collection. Swabs may be taken from the throat, nasal
passage, or nasopharynx. Both swabs may be placed in the same viral
transport container.
• Swabs with wooden shafts are unacceptable for testing.
• Calcium alginate swabs are unacceptable for PCR.
For suspected avian influenza (A/H5), include one upper respiratory
tract specimen (throat swab, nasal swab) and one lower respiratory tract

specimen (BAL, tracheal aspirate).
Transportation and Storage:
Specimens should be put into viral transport media and delivered to
the laboratory on ice within 48 hours. Freeze the specimen if transport will
be delayed beyond 48 hours. Freezing and thawing of specimens should
be avoided since this will result in a loss of viability of some viruses, leading
to a decreased sensitivity if culture for other respiratory viruses is desired.

Malaria & other blood parasites
CPT Code: 87207 (Method, Microscopic examination)
Specimen Collection:
Please submit the following information with the specimen:
1. Where has the patient been? When was the date of return to the U.S.?
2. Has the patient been diagnosed with malaria before?
3. Has patient ever had a blood transfusion?
4. What medication has the patient received? How often? Last dose?
5. When was the blood drawn? Was patient symptomatic at the time?
6. What is the periodicity of the fever?
Peripheral Blood is best collected between paroxysms and before
treatment. Parasites begin to distort within 10 - 12 hours and disappear 2 -
3 days after treatment with chloroquine.
Anticoagulants should be avoided. They interfere with adhesion of
blood to the slide, and they interfere with the staining of the parasites.
Blood preserved with EDTA is acceptable, provided that blood films
are prepared within one hour.
We accept premade thick and thin film blood smears for malaria
confirmation.
Transportation and Storage:
Immediately transport suspected malaria blood smears to the
laboratory at room temperature.

Measles RT-PCR
CPT Code:                 (Method, real-time PCR)
Specimen collection:

1. Throat, Nasal, Nasopharyngeal collected within 7 days onset of symptoms
      collected in viral transport media
   2. Urine samples collected within 10 days of onset
   3. Store samples at 20 C to 80 C or -200 C if extraction is not performed within
      72 hours

Mumps RT-PCR
CPT Code:               (Method, real-time PCR)
Specimen Collection
      1. Buccal, Throat, and Nasopharyngeal aspirates collected within 3 days
         onset of symptoms using Dacron swabs
      2. Insert swabs into viral transport media
      3. Store samples at 20o C to 80o C or -200o C if extraction is not
         performed within 72 hours

Miscellaneous Source Culture (genital, wound, ear, eye, etc.)
CPT Code: 87070 (Method, Culture)
Specimen Collection:
Miscellaneous source specimens include swabs from the ear,
mastoids, accessory sinus, and superficial wounds and lesions.
1. Specimens should be obtained before antimicrobial agents have been
administered.
2. Material should be collected where suspected organisms are most likely
to be found. The “active” portion of the wound should be sampled.
3. Swabs are not the ideal specimens for wound cultures, but they are most
often used. Avoid cotton swabs; they may be toxic to some organisms.
4. When collecting a wound specimen it is important to avoid contaminating
the specimen with microorganisms from the skin, mucous membrane or
external environment. Detritus and medications should be removed with
a sponge soaked in sterile saline followed by 70% alcohol.
Transportation and Storage:
Transport to the laboratory in Amies charcoal transport media at room
temperature within 72 hours.

Mycobacterium tuberculosis PCR - GeneXpert MTB/RIFampin
resistance
CPT Code: 87798 (Method, Real-time PCR)

Specimen Collection:
Sputum (induced or expectorated), bronchial specimens (e.g.,
bronchoalveolar lavage or aspirates) or tracheal aspirates. The efficacy of
this test has not been demonstrated using other clinical specimens (e.g.,
blood, CSF, tissue, urine, or stool). However, we may perform testing of
these specimens upon request, and qualify the result with an appropriate
note.
The test is performed on patients who are suspected of pulmonary
TB based on clinical evaluation and who have not received anti-tuberculosis
therapy, have received less than 7 days of such therapy, or have not
received such therapy in the last 12 months.
Transportation and Storage:
Specimens must be collected in sterile plastic containers, and
stored at 2° - 8ºC until transported or processed. Transport specimens to
the laboratory within 24 hours.

Norovirus PCR
CPT Code: 87798 x 2 (Method, real-time PCR)
Specimen Collection:
This test is not FDA approved and is for research use only.
Stool specimens should be collected in a clean, sterile container
(e.g. urine cup) during the acute phase of illness (48 - 72 hours of diarrhea
onset). C&S transport medium may be used if a sterile container is not
available.
Transportation and Storage:
Specimens are stored at 4o C, and transport to the laboratory within
7 days of collection. Do not freeze specimens.

Ova & Parasite Screen (Stool)
CPT Code: 87177 (Method, Concentration & microscopic examination)
88313 (Trichrome stain)
Specimen Collection:
Fresh (unpreserved) or formalin preserved fecal specimens are

required to detect helminth cysts (eggs) and larvae. Fresh specimens must
be examined in the laboratory within 4 hours of passage. In most cases
(where the time interval will be longer), multiple specimens will be submitted
in 5 - 10% formalin.
Patients should collect 3 separate specimens over a period of 7 – 10 days to
maximize recovery of parasites.
Transportation and Storage:
Store and transport at room temperature within 10 days.

Parasitic Arthropod/Worm Identification
CPT Code: 87168 (Method, Microscopic/Macroscopic examination)
Specimen Collection:
Insects, mites, spiders, and ticks suspected of parasitizing a patient
may be collected in a clean, sterile, screw-cap container. Do not add
alcohol, formalin, or other preservatives. Do not kill the arthropod by
freezing, CO2, etc.
Ticks can be identified to determine if they are of the species
known to carry Lyme disease. Remove ticks by grasping the tick as close to
the skin as possible with fine tweezers. Gently pull the tick away from the
skin with a steady motion. Avoid crushing the tick’s body.
Transportation and Storage:
Store and transport at room temperature as soon as possible.

Pinworm screen (Paddle Collection slide)
CPT Code: 87172 (Method, Microscopic examination)
Specimen Collection:
Specimens are best obtained an hour or two after the patient goes
to sleep or just after waking and before a bath or bowel movement. The
paddle’s sticky side should be pressed against several areas of the perianal
region while spreading open the perianal folds. The paddle is then placed
back into the transport tube and the cap tightened. Multiple specimens may
be necessary.
Transportation and Storage:
Transport at 4ºC within 24 hours. Parasite eggs will deteriorate
rapidly in heat. Specimens should be refrigerated at 4ºC if examination is to
be delayed.

QuantiFERON®
CPT Code: 86849 (Method, Enzyme immunoassay)
Specimen Collection:
The QuantiFERON collection kit uses the following 4 collection tubes:
1. Nil Control (Grey cap)
2. TB 1 Antigen (Green cap)
3. TB 2 Antigen (yellow cap)
4. Mitogen Control (Purple cap)

Antigens have been dried onto the inner wall of the blood collection
tubes, so it is essential that the contents of the tubes be thoroughly
mixed with the blood. The test requires live white blood cells, so tubes
must be transferred to a 37°C incubator as soon as possible, and within 16
hours of collection.
To ensure valid test results, follow the procedures below:
1. For each subject collect 1 ml of blood by venipuncture directly into each
of the QuantiFERON blood collection tubes.
2. As 1 ml tubes draw blood relatively slowly, keep the tube on the needle
for 2 - 3 seconds once the tube appears to have completed filling, to
ensure that the correct volume is drawn.
3. The black mark on the side of the tubes indicates the 1 ml fill volume.
QuantiFERON blood collection tubes have been validated for volumes
ranging from 0.8 to 1.2 ml. If the level of blood in any tube is not close to
the indicator line, it is recommended to obtain another blood sample.
4. If a “butterfly needle” is being used to collect blood, a “purge” tube
should be used to ensure that the tubing is filled with blood prior to the
QuantiFERON tubes being used.
5. The tubes must be shaken 10 times firmly enough to mix the blood with the
antigen that has been dried onto the walls of the blood collection tubes.
6. Alternatively a single Lithium Heparin green top tube can be used to collect
enough blood to fill the four TB gold tubes (0.8 to 1.2 ml per tube). Lithium
Heparin tubes can only be stored for only 12 hours at room temperature

Transportation and Storage:
QuantiFERON collection tubes must be transported to the laboratory

within 16 hours of collection (12 hours for Lithium Heparin) at ambient
temperature (22°C +/- 5°C). DO NOT REFRIGERATE OR FREEZE!

Rabies (Non-Human Specimens Only)
CPT Code: None (Method, Microscopic examination w/ fluorescent
antibody stain)
Specimen Collection:
   a. Specimens received as whole animal heads. Whole brains are acceptable
      specimens and are generally received from large animals.

Transportation and Storage:
Specimens should be transported to the laboratory as soon as possible and need
to be refrigerated before and after they are received. Specimens are not to be
frozen.

Respiratory Virus Antigen Screen by DFA
CPT Code: 87253 (Method, Fluorescent antibody stain)
Specimen Collection:
Nasal aspirates or nasal washes are preferred. Nasopharyngeal
swabs and throat swabs can also be tested. Cotton or Dacron swabs on a
plastic or wire shaft are acceptable for testing. Calcium alginate swabs
and swabs with wooden shafts are NOT ACCEPTABLE for testing.
The following viruses can be detected:
• Adenovirus
• Influenza A & B
• Parainfluenza 1, 2 & 3
• RSV (respiratory Syncytial virus)
Transportation and Storage:
Specimens should be placed in viral transport media and delivered
to the laboratory at 4o C within 48 hours.
Freeze the specimen if transport will be delayed beyond 48 hours.
Avoid freezing and thawing of specimens, since this will result in a loss of
viability for some viruses, leading to decreased test sensitivity.

RPR (Syphilis Screen Serum)

CPT Code: 86592 (Method, Agglutination), 86593 (Method, Titer)
Specimen Collection:
Collect venous blood in a 9.5 ml serum separator tube (tiger top
Vacutainer®) and allow the specimen to clot before refrigeration.
Transportation and Storage:
Store and transport at 4o C within 8 days of collection.

SARS Coronavirus
CPT Code: Not assigned (Method, Polymerase chain reaction PCR)
Specimen Collection:
Upper Respiratory Tract
•        Nasopharyngeal (NP): Insert a swab into the nostril parallel to the palate. Leave
the swab in place for a few seconds to absorb secretions. Swab both nasopharyngeal areas
with the same swab. Place swabs immediately into sterile viral transport media.
•        Oropharyngeal (OP) (e.g., throat swab): Swab the posterior pharynx, avoiding the
tongue. Place swab immediately into sterile viral transport media. Use only synthetic
fiber swabs with plastic shafts.
•        Keep NP and OP specimens in separate vials.
•        Wash or aspirate: Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum
collection cup or sterile dry container.
Lower respiratory
•        Bronchoalveolar lavage, tracheal aspirate: Collect 2-3 mL into a sterile, leak-
proof, screw-cap sputum collection cup or sterile dry container.
•        Sputum: Have the patient rinse the mouth with water and then expectorate deep
cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or
sterile dry container. Do not collect sputum if it must be induced.
Storage: Refrigerate at 2-8⁰ C.
Transport: Transport to SCPHL on cold pack
Test Turn-Around Time: 24 to 72 hours upon arrival at SCPHL, Sacramento.

Select Agent Identification / Rule-Out
CPT Code: None (Method, Culture and PCR)
Specimen Collection:
Collect specimens as appropriate for the source and organism
suspected. Please refer to the submission guidelines under “Culture for
Identification (Bacterial, Fungal, Mycobacterial)”.
Please fill out a Title 17 submission form with this specimen type.

Transportation and Storage:
Transport as appropriate for the source and organism suspected.
SPECIAL FEDERAL REGULATIONS APPLY TO REQUESTS FOR
SELECT AGENT RULE-OUT. CALL THE LABORATORY IMMEDIATELY
IF YOU SUSPECT YOU HAVE ISOLATED A SELECT AGENT, BEFORE
SENDING ANY CULTURE ISOLATE.

Shiga Toxin Test Only
CPT Code: 87427 (Method, Enzyme immunoassay)
Specimen Collection:
Stool specimen submitted in GN or MAC broth.
Transportation and Storage:
Transport within 24 hours at room temperature; store at 4o C if
transportation will be delayed longer than 4 days. Please see the “Enteric
Screen” entry for culture-specific instructions.

Sputum - Comprehensive Bacterial Culture and Gram Stain
CPT Code: 87070 (Method, Culture), 87205 (Method, Gram stain)
Specimen Collection:
1 - 3 ml of sputum material collected from a deep cough should be
submitted in a sterile container. A specimen that is obviously saliva is
unsatisfactory for examination.
Transportation and Storage:
Specimens may be refrigerated at 4ºC up to 24 hours after
collection if necessary. Transport to the laboratory at 4ºC within 24 hours.

Streptococcus Group A Screen (silica gel beads)
CPT Code: 87081 (Method, Culture), 87147 (Method Agglutination)
Specimen Collection:
A sterile swab is rubbed over the tonsillar area and posterior
pharynx, and any inflamed or exudative areas. Avoid contact with the
tongue or cheek to avoid contamination with normal bacterial flora.
Transportation and Storage:
Survival of streptococci is optimal when silica gel transport media is
used. However, Amies transport medium may be used. Transport to the

laboratory at room temperature within 24 hours.

TP-PA - Confirmation for Reactive RPRs (Serum)
CPT Code: 86781 (Method, Particle Agglutination)
Specimen Collection:
Collect serum in a 9.5 ml serum separator tube (tiger top
Vacutainer®) and allow to clot before refrigeration. Plasma from tubes
using EDTA, sodium citrate or heparin as anticoagulants may be used if
serum cannot be obtained.
Transportation and Storage:
Store patient specimens at 2° - 8°C if testing will be performed
within 5 days. Specimens can be frozen and thawed once for longer
storage. Transport at 4ºC.

Urine Culture
CPT Code: 87086 (Method Culture with quantification)
Specimen Collection:
Clean-catch, midstream urine should be collected to avoid
contamination with flora from the urethra, vagina, prostate, or perineum.
First-void morning urine should be collected when possible. If specimen
transport will be delayed more than 24 hours, a Urine Preservative (UPP)
container is available that extends transport time up to 72 hours.
Transportation and Storage:
For best results, urine specimens should be cultured within 2 hours
of collection, or stored at 4ºC and cultured within 24 hours. Specimens
collected in Urine Preservative (UPP) containers should be stored and
transported at 4ºC, and reach the laboratory within 72 hours.

Varicella-Zoster Virus (VZV) PCR (fresh exudate / scab)
CPT Code: 87798 (Method, Polymerase Chain Reaction)
Specimen Collection:
Cellular material from the base of fresh lesions may be used. Basal,
parabasal, and intermediate cells scraped from the lesion’s base are
appropriate samples to collect. Remove the cap from a fresh lesion or

vesicle. Using a Dacron swab moistened in saline or transport solution,
vigorously scrape the base of the lesion to collect cellular material. Avoid
contamination with blood. Place swab in viral transport medium and mix
well to dislodge cellular material.
Scabs removed from suspect lesions may also be submitted in a
dry sterile container.
Transportation and Storage:
Store and transport to the laboratory at 4°C within 48 hours.

Viral Isolation / Detection (Miscellaneous)
CPT Code: 87252 (Method, Culture)
Specimen Collection:
Please contact the laboratory for information on isolation of viruses

West Nile Virus (WNV) Antibody Screen & Confirmation
CPT Code: 86789 (Method, Enzyme immunoassay)
86788 (Immuofluorescent antibody (IFA) confirmation)
Specimen Collection:
Collect venous blood in a 9.5 ml serum separator tube (tiger top
Vacutainer®), or collect a plasma specimen in a sterile tube with anticoagulant.
CSF can also be tested; collect at least 0.5 ml in a sterile
container.
CSF is tested at the State Laboratory; turn-around time is variable.
CSF specimens negative for WNV are also tested for Enterovirus.
Transportation and Storage:
Serum or plasma may be used, and may be stored at 2° - 8°C for
up to 5 days. Separated serum may be frozen at -20°C or below for
extended periods. CSF must be stored at -20°C, and transported frozen.